In the case of San Francisco it is a state law that limits cities to charging only as much as it costs to administer the program. San Francisco cannot have responsive residential parking under state law.
I guess the solution would be to make these spots 2/4 hr parking, instead of permanent overnight parking for all. Or remove parking all together and make it easy to build private parking lots.
SF's lack of grade separated transport outside the narrow BART corridor also makes it hard to convince people out of driving. Buses and trams aren't acceptable alternatives for a city as rich and dynamic as SF.